If you are using a deep sand bed you vacuum only the top 3/4 inch or so. If it's just enough sand to cover the bottom, you can vacuum all the way down.
How often you do this depends upon a lot of factors, and about all you can do is examine the sand from time to time, and if it's become a "dirt trap" vacuum it.
You'll usually find that the worst places for accumulating dirt are the corners, places of low flow, and the open area in front. You usually don't need to move LR and get under there.
Yes, the process of vacuuming the tank does remove a lot of bacteria, but this is not a problem because first you don't do the entire sandbed, just those bad areas, and second you have enough live rock in the system, 1 to 1 1/2 lbs per gallon.
You'll also discover that most LFSs are clueless when it comes to reef systems, so don't use them as your primary source of advice. It's ok to ask them, but confirm their answers. "Trust, but verify."
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